CatFish Fecal Samples Analysis March 20, 2020
Waseem (Fernando Lab)
library(tibble)
mapping_data= as.tibble(sample_data(final_ps_NO_Outlier_NO_singelton))
mapping_data$Sampling_day= as.factor(mapping_data$Sampling_day)
mapping_data## # A tibble: 170 x 17
## SampleID plate_number sample_type Fish_ID Sample_Number Fish_ID_sample_…
## <int> <int> <fct> <int> <int> <fct>
## 1 100 2 catfish_po… 15454 3 15454-3
## 2 101 2 catfish_po… 15454 7 15454-7
## 3 102 2 catfish_po… 15455 1 15455-1
## 4 103 2 catfish_po… 15455 2 15455-2
## 5 104 2 catfish_po… 15455 3 15455-3
## 6 105 2 catfish_po… 15455 5 15455-5
## 7 106 2 catfish_po… 15455 6 15455-6
## 8 107 2 catfish_po… 15455 7 15455-7
## 9 108 2 catfish_po… 15456 5 15456-5
## 10 109 2 catfish_po… 15456 7 15456-7
## # … with 160 more rows, and 11 more variables: Sampling_day <fct>, date <fct>,
## # tank2 <fct>, tank <fct>, temperature <dbl>, start_length <dbl>,
## # start_weight <dbl>, end_length <int>, end_weight <dbl>,
## # change_In_Length <dbl>, change_In_weight <dbl>#Outlier 98 I remove the sample 98 because it was the only Outlier 
#change in weight and Length
## Using Sampling_day, tank as id variables
## Using Sampling_day, tank as id variables
#Beta Diversity (unifrac), Alpha Diversity (rarefy @ 1044) and Abundance
##
## Call:
## adonis(formula = final_ps_NO_Outlier_NO_singelton_bray ~ tank + Sampling_day + Fish_ID, data = sampledf)
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## tank 3 1.690 0.56345 2.7447 0.04231 0.001 ***
## Sampling_day 6 5.016 0.83594 4.0721 0.12556 0.001 ***
## Fish_ID 1 0.600 0.60044 2.9249 0.01503 0.008 **
## Residuals 159 32.640 0.20529 0.81710
## Total 169 39.947 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#observed bacterial species for each Fish (15351,15352 etc) over time 
library(phyloseq)
library(devtools)
#remotes::install_github("vmikk/metagMisc")
library("metagMisc")
tank_phyloseqs_proportions= phyloseq_sep_variable(final_ps_NO_Outlier_NO_singelton_Proportions, "tank")
#tank1c
tank_phyloseqs_proportions$`1c`## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 1403 taxa and 39 samples ]
## sample_data() Sample Data: [ 39 samples by 17 sample variables ]
## tax_table() Taxonomy Table: [ 1403 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 1403 tips and 1402 internal nodes ]#tank2c
tank_phyloseqs_proportions$`2c`## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 2268 taxa and 45 samples ]
## sample_data() Sample Data: [ 45 samples by 17 sample variables ]
## tax_table() Taxonomy Table: [ 2268 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 2268 tips and 2267 internal nodes ]#tank3b
tank_phyloseqs_proportions$`3b`## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 1788 taxa and 43 samples ]
## sample_data() Sample Data: [ 43 samples by 17 sample variables ]
## tax_table() Taxonomy Table: [ 1788 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 1788 tips and 1787 internal nodes ]#tank3c
tank_phyloseqs_proportions$`3c`## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 1021 taxa and 43 samples ]
## sample_data() Sample Data: [ 43 samples by 17 sample variables ]
## tax_table() Taxonomy Table: [ 1021 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 1021 tips and 1020 internal nodes ]##tank 1c # Beta Diversity and Hierachical clustering tank 1c & similarity percentages (SIMPER) 
##
## Call:
## adonis(formula = final_ps_bray ~ Sampling_day + Fish_ID, data = sampledf)
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## Sampling_day 5 2.7200 0.54401 1.8302 0.21512 0.001 ***
## Fish_ID 1 0.4123 0.41232 1.3872 0.03261 0.051 .
## Residuals 32 9.5119 0.29725 0.75227
## Total 38 12.6442 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 3 3 3 3 3 3
## [26] 3 5 5 5 5 5 5 5 7 7 7 7 7 21
## Levels: 0 1 3 5 7 21
## cumulative contributions of most influential species:
##
## $`0_3`
## ASV_1 ASV_2 ASV_4 ASV_5 ASV_8 ASV_14 ASV_13 ASV_6
## 0.2249376 0.3417685 0.4204450 0.4933250 0.5198915 0.5453851 0.5685554 0.5897862
## ASV_17 ASV_7 ASV_22 ASV_10 ASV_29 ASV_52 ASV_49 ASV_42
## 0.6085536 0.6233455 0.6372845 0.6505314 0.6607156 0.6708248 0.6806765 0.6897858
## ASV_21 ASV_32
## 0.6980445 0.7056588
##
## $`0_5`
## ASV_1 ASV_2 ASV_4 ASV_17 ASV_6 ASV_48 ASV_7 ASV_9
## 0.2284310 0.3676688 0.4527429 0.4793300 0.5021091 0.5235319 0.5396229 0.5547443
## ASV_22 ASV_10 ASV_38 ASV_14 ASV_29 ASV_49 ASV_42 ASV_21
## 0.5697497 0.5845196 0.5986399 0.6126710 0.6239597 0.6346149 0.6445139 0.6534327
## ASV_32 ASV_24 ASV_5 ASV_28 ASV_23 ASV_80 ASV_39
## 0.6618173 0.6692423 0.6760344 0.6825435 0.6889924 0.6953535 0.7016836
##
## $`0_7`
## ASV_1 ASV_2 ASV_4 ASV_6 ASV_7 ASV_22 ASV_14 ASV_10
## 0.2895727 0.3900952 0.4641156 0.4841549 0.4982357 0.5114955 0.5240067 0.5365030
## ASV_33 ASV_55 ASV_29 ASV_49 ASV_57 ASV_42 ASV_303 ASV_304
## 0.5469633 0.5570035 0.5666488 0.5759278 0.5849490 0.5935800 0.6020140 0.6104038
## ASV_61 ASV_315 ASV_21 ASV_63 ASV_331 ASV_334 ASV_32 ASV_345
## 0.6185559 0.6267021 0.6344754 0.6419381 0.6493981 0.6568361 0.6640847 0.6711905
## ASV_346 ASV_347 ASV_352 ASV_354 ASV_332
## 0.6782521 0.6852916 0.6921982 0.6990827 0.7058122
##
## $`0_1`
## ASV_1 ASV_2 ASV_30 ASV_4 ASV_5 ASV_18 ASV_3 ASV_6
## 0.2293697 0.3519091 0.4517204 0.5312088 0.5796240 0.6165966 0.6437652 0.6637149
## ASV_10 ASV_14 ASV_7
## 0.6806650 0.6966248 0.7113071
##
## $`0_21`
## ASV_1 ASV_2 ASV_4 ASV_38 ASV_54 ASV_3 ASV_6 ASV_7
## 0.2703207 0.3939574 0.4957436 0.5579093 0.5898708 0.6183098 0.6460004 0.6654713
## ASV_22 ASV_14
## 0.6836646 0.7009467
##
## $`3_5`
## ASV_1 ASV_2 ASV_5 ASV_17 ASV_8 ASV_13 ASV_48 ASV_14
## 0.2080986 0.3516990 0.4358519 0.4798221 0.5105480 0.5367477 0.5601299 0.5802764
## ASV_38 ASV_9 ASV_52 ASV_91 ASV_27 ASV_60 ASV_80 ASV_16
## 0.5956908 0.6096687 0.6215892 0.6290171 0.6360618 0.6430169 0.6499643 0.6565571
## ASV_3 ASV_443 ASV_30 ASV_120 ASV_426 ASV_94 ASV_715 ASV_12
## 0.6631219 0.6691470 0.6751359 0.6809289 0.6864729 0.6919272 0.6973596 0.7027128
##
## $`3_7`
## ASV_1 ASV_2 ASV_5 ASV_8 ASV_13 ASV_17 ASV_14 ASV_33
## 0.2884237 0.3805331 0.4528457 0.4791457 0.5015196 0.5200789 0.5371879 0.5483895
## ASV_55 ASV_52 ASV_57 ASV_303 ASV_304 ASV_61 ASV_315 ASV_63
## 0.5592823 0.5694858 0.5793229 0.5883675 0.5973646 0.6062400 0.6149759 0.6230640
## ASV_331 ASV_334 ASV_345 ASV_346 ASV_347 ASV_352 ASV_354 ASV_332
## 0.6310641 0.6390404 0.6466606 0.6542333 0.6617823 0.6691889 0.6765717 0.6837884
## ASV_16 ASV_373 ASV_71
## 0.6907236 0.6976554 0.7045728
##
## $`3_1`
## ASV_1 ASV_2 ASV_30 ASV_5 ASV_18 ASV_3 ASV_8 ASV_14
## 0.2252776 0.3496842 0.4534481 0.5571988 0.5938589 0.6213485 0.6479664 0.6726263
## ASV_13 ASV_17
## 0.6961268 0.7175684
##
## $`3_21`
## ASV_1 ASV_2 ASV_5 ASV_38 ASV_8 ASV_54 ASV_13 ASV_3
## 0.2509058 0.4014086 0.5007299 0.5669712 0.6028819 0.6369388 0.6674926 0.6962123
## ASV_17
## 0.7215537
##
## $`5_7`
## ASV_1 ASV_2 ASV_17 ASV_48 ASV_38 ASV_33 ASV_9 ASV_55
## 0.2942730 0.4044326 0.4320884 0.4548479 0.4697171 0.4839792 0.4978134 0.5101392
## ASV_57 ASV_303 ASV_304 ASV_61 ASV_315 ASV_63 ASV_331 ASV_334
## 0.5212655 0.5314584 0.5415978 0.5516048 0.5614500 0.5705944 0.5796102 0.5885992
## ASV_345 ASV_346 ASV_347 ASV_352 ASV_354 ASV_332 ASV_373 ASV_71
## 0.5971869 0.6057212 0.6142287 0.6225756 0.6308958 0.6390288 0.6468407 0.6546351
## ASV_70 ASV_383 ASV_76 ASV_398 ASV_83 ASV_80 ASV_412
## 0.6623669 0.6698578 0.6772537 0.6844236 0.6914426 0.6982794 0.7050747
##
## $`5_1`
## ASV_1 ASV_2 ASV_30 ASV_5 ASV_18 ASV_3 ASV_17 ASV_48
## 0.2266033 0.3721551 0.4796750 0.5314437 0.5705545 0.6001647 0.6290179 0.6506339
## ASV_9 ASV_38 ASV_10 ASV_14
## 0.6687566 0.6830042 0.6959190 0.7080454
##
## $`5_21`
## ASV_2 ASV_1 ASV_38 ASV_17 ASV_54 ASV_48 ASV_3 ASV_9
## 0.2404446 0.4231687 0.4883950 0.5326290 0.5703187 0.6064007 0.6423362 0.6635767
## ASV_80 ASV_443 ASV_696 ASV_120
## 0.6742907 0.6835867 0.6928566 0.7017945
##
## $`7_1`
## ASV_1 ASV_2 ASV_30 ASV_5 ASV_18 ASV_3 ASV_10 ASV_14
## 0.2883433 0.3932031 0.4870067 0.5323112 0.5663341 0.5915973 0.6028901 0.6137749
## ASV_33 ASV_55 ASV_57 ASV_303 ASV_304 ASV_61 ASV_315 ASV_63
## 0.6246440 0.6347531 0.6438363 0.6523283 0.6607757 0.6689837 0.6771860 0.6846999
## ASV_331 ASV_334 ASV_345
## 0.6922112 0.6997002 0.7068549
##
## $`7_21`
## ASV_1 ASV_2 ASV_38 ASV_54 ASV_3 ASV_33 ASV_55 ASV_57
## 0.3105460 0.4776467 0.5388606 0.5703327 0.5976816 0.6118157 0.6254014 0.6376082
## ASV_303 ASV_304 ASV_61 ASV_315 ASV_63 ASV_331
## 0.6490206 0.6603731 0.6714038 0.6824268 0.6925248 0.7026192
##
## $`1_21`
## ASV_1 ASV_2 ASV_30 ASV_38 ASV_5 ASV_18
## 0.2707752 0.4089981 0.5381533 0.6011320 0.6640417 0.7110939##tank 2c # Beta Diversity and Hierachical clustering tank 2c & similarity percentages (SIMPER)
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 2268 taxa and 45 samples ]
## sample_data() Sample Data: [ 45 samples by 17 sample variables ]
## tax_table() Taxonomy Table: [ 2268 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 2268 tips and 2267 internal nodes ]
##
## Call:
## adonis(formula = final_ps_bray ~ Sampling_day + Fish_ID, data = sampledf)
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## Sampling_day 6 2.5936 0.43227 1.3897 0.17931 0.004 **
## Fish_ID 1 0.3617 0.36166 1.1627 0.02500 0.199
## Residuals 37 11.5090 0.31105 0.79568
## Total 44 14.4642 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] 3 35 0 1 3 7 21 35 7 35 0 21 35 0 21 0 3 5 0 1 21 3 5 7 0
## [26] 7 35 0 21 35 0 1 3 5 21 35 0 1 35 0 3 7 21 5 0
## Levels: 0 1 3 5 7 21 35## [1] 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 3 3 3 3 3 3 5 5 5 5
## [26] 7 7 7 7 7 21 21 21 21 21 21 21 35 35 35 35 35 35 35 35
## Levels: 0 1 3 5 7 21 35
## [1] 45 17## [1] 45 17## cumulative contributions of most influential species:
##
## $`5_0`
## ASV_1 ASV_2 ASV_4 ASV_34 ASV_13 ASV_3 ASV_26 ASV_18
## 0.2863347 0.4177174 0.4575488 0.4808084 0.5037789 0.5267439 0.5453065 0.5603975
## ASV_6 ASV_33 ASV_73 ASV_99 ASV_7 ASV_121 ASV_124 ASV_38
## 0.5731826 0.5855582 0.5972368 0.6086703 0.6188564 0.6283868 0.6377273 0.6463001
## ASV_135 ASV_109 ASV_168 ASV_158 ASV_22 ASV_177 ASV_180 ASV_175
## 0.6546488 0.6620780 0.6693295 0.6765609 0.6835705 0.6901881 0.6967411 0.7032557
##
## $`5_3`
## ASV_1 ASV_2 ASV_4 ASV_3 ASV_34 ASV_13 ASV_54 ASV_18
## 0.2811521 0.4792805 0.5171194 0.5530435 0.5754074 0.5971851 0.6130877 0.6277135
## ASV_33 ASV_73 ASV_6 ASV_99 ASV_7 ASV_121 ASV_124 ASV_135
## 0.6407125 0.6523876 0.6636399 0.6739221 0.6832298 0.6915591 0.6998251 0.7072800
##
## $`5_35`
## ASV_1 ASV_2 ASV_4 ASV_13 ASV_34 ASV_7 ASV_18 ASV_33
## 0.2566195 0.4093402 0.4605237 0.4848168 0.5079875 0.5273662 0.5424352 0.5547759
## ASV_6 ASV_73 ASV_99 ASV_20 ASV_121 ASV_124 ASV_135 ASV_109
## 0.5664715 0.5779022 0.5885554 0.5978045 0.6064343 0.6149985 0.6227223 0.6296768
## ASV_22 ASV_138 ASV_168 ASV_158 ASV_28 ASV_177 ASV_12 ASV_175
## 0.6365707 0.6433622 0.6501043 0.6567006 0.6630114 0.6691043 0.6751795 0.6811920
## ASV_180 ASV_21 ASV_163 ASV_174
## 0.6871882 0.6929265 0.6985218 0.7040868
##
## $`5_1`
## ASV_1 ASV_2 ASV_9 ASV_4 ASV_34 ASV_13 ASV_10 ASV_33
## 0.3254215 0.4456450 0.4885336 0.5220691 0.5482736 0.5741326 0.5956718 0.6127300
## ASV_18 ASV_5 ASV_6 ASV_73 ASV_99 ASV_7 ASV_121
## 0.6297862 0.6434871 0.6568051 0.6693703 0.6814183 0.6918865 0.7016461
##
## $`5_7`
## ASV_1 ASV_2 ASV_3 ASV_6 ASV_8 ASV_65 ASV_4 ASV_34
## 0.2177764 0.3093163 0.3576529 0.3988430 0.4369119 0.4627252 0.4870969 0.5072371
## ASV_62 ASV_13 ASV_23 ASV_18 ASV_24 ASV_33 ASV_73 ASV_99
## 0.5265178 0.5453346 0.5622924 0.5791065 0.5910017 0.6020766 0.6114704 0.6202306
## ASV_7 ASV_121 ASV_124 ASV_135 ASV_283 ASV_46 ASV_222 ASV_22
## 0.6285496 0.6356460 0.6426885 0.6490399 0.6552719 0.6610221 0.6667384 0.6724309
## ASV_109 ASV_168 ASV_158 ASV_177 ASV_175 ASV_180
## 0.6781173 0.6836614 0.6890857 0.6940959 0.6990401 0.7039709
##
## $`5_21`
## ASV_1 ASV_11 ASV_2 ASV_6 ASV_4 ASV_7 ASV_34 ASV_13
## 0.2907495 0.3876640 0.4837355 0.5202260 0.5550303 0.5785131 0.5983734 0.6177698
## ASV_24 ASV_21 ASV_23 ASV_18 ASV_33 ASV_22 ASV_32
## 0.6335672 0.6490992 0.6631434 0.6766345 0.6881784 0.6995195 0.7091178
##
## $`0_3`
## ASV_1 ASV_2 ASV_3 ASV_4 ASV_54 ASV_26 ASV_38 ASV_12
## 0.3331047 0.5407862 0.5919523 0.6240325 0.6423142 0.6602689 0.6701381 0.6765544
## ASV_6 ASV_14 ASV_28 ASV_66 ASV_9
## 0.6827531 0.6882556 0.6934419 0.6984788 0.7034621
##
## $`0_35`
## ASV_1 ASV_2 ASV_4 ASV_3 ASV_26 ASV_7 ASV_20 ASV_38
## 0.3060405 0.4647875 0.5111045 0.5368208 0.5578039 0.5738752 0.5839646 0.5926509
## ASV_13 ASV_28 ASV_138 ASV_17 ASV_35 ASV_12 ASV_21 ASV_55
## 0.6013105 0.6093589 0.6162668 0.6229265 0.6295575 0.6358953 0.6421246 0.6480522
## ASV_163 ASV_174 ASV_54 ASV_169 ASV_50 ASV_57 ASV_74 ASV_66
## 0.6537647 0.6594250 0.6650500 0.6705909 0.6758758 0.6810917 0.6862700 0.6913843
## ASV_9 ASV_39
## 0.6963461 0.7011135
##
## $`0_1`
## ASV_1 ASV_2 ASV_9 ASV_3 ASV_26 ASV_10 ASV_4 ASV_5
## 0.3424293 0.4903331 0.5406132 0.5720328 0.5945095 0.6167669 0.6363220 0.6505145
## ASV_33 ASV_38 ASV_53 ASV_55 ASV_98 ASV_54
## 0.6624049 0.6731061 0.6810986 0.6889641 0.6959738 0.7029035
##
## $`0_7`
## ASV_1 ASV_2 ASV_3 ASV_6 ASV_8 ASV_65 ASV_62 ASV_23
## 0.2802434 0.3801416 0.4370157 0.4750818 0.5123121 0.5375614 0.5564209 0.5728002
## ASV_26 ASV_4 ASV_24 ASV_18 ASV_38 ASV_283 ASV_222 ASV_46
## 0.5871904 0.6008452 0.6125437 0.6220539 0.6289228 0.6350185 0.6406098 0.6460915
## ASV_13 ASV_54 ASV_32 ASV_106 ASV_66 ASV_55 ASV_9 ASV_110
## 0.6511950 0.6556432 0.6599976 0.6640486 0.6680990 0.6720405 0.6759462 0.6797125
## ASV_20 ASV_74 ASV_156 ASV_12 ASV_436 ASV_57
## 0.6834613 0.6871129 0.6906038 0.6940843 0.6975428 0.7009974
##
## $`0_21`
## ASV_1 ASV_2 ASV_11 ASV_6 ASV_4 ASV_7 ASV_3 ASV_24
## 0.3193772 0.4230103 0.5204406 0.5545395 0.5861405 0.6073487 0.6269916 0.6431863
## ASV_21 ASV_26 ASV_23 ASV_32 ASV_22
## 0.6590680 0.6745847 0.6887856 0.6980894 0.7072141
##
## $`3_35`
## ASV_1 ASV_2 ASV_4 ASV_3 ASV_54 ASV_7 ASV_20 ASV_13
## 0.3086428 0.5324892 0.5777766 0.6158639 0.6318724 0.6467676 0.6554211 0.6637356
## ASV_12 ASV_138 ASV_28 ASV_14 ASV_163 ASV_174
## 0.6714135 0.6780122 0.6841026 0.6901742 0.6956107 0.7010177
##
## $`3_1`
## ASV_1 ASV_2 ASV_3 ASV_9 ASV_4 ASV_10
## 0.3585911 0.5900502 0.6337019 0.6763147 0.6991655 0.7180738
##
## $`3_7`
## ASV_1 ASV_2 ASV_3 ASV_6 ASV_8 ASV_65 ASV_62 ASV_4
## 0.2597132 0.4310583 0.4941593 0.5313953 0.5681842 0.5932780 0.6119125 0.6286272
## ASV_23 ASV_54 ASV_24 ASV_18 ASV_283 ASV_222 ASV_46 ASV_13
## 0.6448242 0.6579188 0.6692052 0.6782630 0.6842861 0.6898108 0.6952151 0.7004346
##
## $`3_21`
## ASV_1 ASV_2 ASV_11 ASV_6 ASV_3 ASV_4 ASV_7 ASV_24
## 0.3064782 0.4897820 0.5834767 0.6162513 0.6471451 0.6776635 0.6978721 0.7131751
##
## $`35_1`
## ASV_1 ASV_2 ASV_9 ASV_4 ASV_10 ASV_7 ASV_5 ASV_33
## 0.3243739 0.4814258 0.5271135 0.5714108 0.5912203 0.6090764 0.6235757 0.6350782
## ASV_20 ASV_13 ASV_3 ASV_138 ASV_163 ASV_98 ASV_174 ASV_28
## 0.6460756 0.6561994 0.6653436 0.6735166 0.6802501 0.6869777 0.6936747 0.7001074
##
## $`35_7`
## ASV_1 ASV_2 ASV_3 ASV_6 ASV_8 ASV_4 ASV_65 ASV_62
## 0.2585903 0.3652670 0.4132635 0.4500226 0.4867535 0.5164493 0.5413672 0.5599793
## ASV_23 ASV_7 ASV_24 ASV_13 ASV_18 ASV_20 ASV_283 ASV_222
## 0.5760550 0.5887461 0.6002547 0.6094974 0.6186659 0.6257401 0.6317559 0.6372740
## ASV_138 ASV_46 ASV_163 ASV_174 ASV_12 ASV_28 ASV_169 ASV_17
## 0.6426651 0.6479127 0.6523542 0.6567717 0.6611422 0.6653940 0.6696259 0.6735632
## ASV_106 ASV_21 ASV_110 ASV_32 ASV_196 ASV_197 ASV_285 ASV_5
## 0.6774064 0.6811376 0.6848546 0.6885637 0.6920173 0.6954563 0.6988783 0.7022968
##
## $`35_21`
## ASV_1 ASV_2 ASV_11 ASV_4 ASV_6 ASV_7 ASV_21 ASV_24
## 0.3105766 0.4201073 0.5174341 0.5600277 0.5931585 0.6205068 0.6369084 0.6528893
## ASV_23 ASV_22 ASV_32 ASV_20 ASV_82
## 0.6668542 0.6761028 0.6849505 0.6936931 0.7022899
##
## $`1_7`
## ASV_1 ASV_2 ASV_3 ASV_8 ASV_6 ASV_9 ASV_65 ASV_62
## 0.3410236 0.4196907 0.4713634 0.5112571 0.5511474 0.5837744 0.6109316 0.6311847
## ASV_23 ASV_10 ASV_24 ASV_5 ASV_18 ASV_33
## 0.6485407 0.6626849 0.6748369 0.6850610 0.6949047 0.7021033
##
## $`1_21`
## ASV_1 ASV_11 ASV_2 ASV_6 ASV_9 ASV_4 ASV_7 ASV_24
## 0.3602850 0.4706084 0.5544941 0.5920171 0.6292908 0.6545353 0.6781983 0.6962114
## ASV_21
## 0.7133035
##
## $`7_21`
## ASV_1 ASV_11 ASV_2 ASV_6 ASV_3 ASV_8 ASV_65 ASV_4
## 0.2653252 0.3495644 0.4147984 0.4648629 0.5084955 0.5431914 0.5667289 0.5861158
## ASV_23 ASV_24 ASV_7 ASV_62 ASV_21 ASV_18 ASV_32 ASV_22
## 0.6054640 0.6246345 0.6429655 0.6605479 0.6736087 0.6838193 0.6928866 0.7008214##tank 3b # Beta Diversity and Hierachical clustering tank 3b & similarity percentages (SIMPER)
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 1788 taxa and 43 samples ]
## sample_data() Sample Data: [ 43 samples by 17 sample variables ]
## tax_table() Taxonomy Table: [ 1788 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 1788 tips and 1787 internal nodes ]
##
## Call:
## adonis(formula = final_ps_bray ~ Sampling_day + Fish_ID, data = sampledf)
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## Sampling_day 6 3.2857 0.54761 1.8083 0.23038 0.001 ***
## Fish_ID 1 0.3771 0.37715 1.2454 0.02644 0.142
## Residuals 35 10.5989 0.30282 0.74317
## Total 42 14.2617 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## cumulative contributions of most influential species:
##
## $`0_1`
## ASV_2 ASV_1 ASV_8 ASV_11 ASV_3 ASV_7 ASV_4 ASV_37
## 0.1899658 0.3216521 0.3904139 0.4446404 0.4850127 0.5201208 0.5500915 0.5785007
## ASV_14 ASV_13 ASV_9 ASV_6 ASV_41 ASV_21 ASV_107 ASV_29
## 0.6009140 0.6229622 0.6421749 0.6589597 0.6732703 0.6850165 0.6947209 0.7042558
##
## $`0_3`
## ASV_2 ASV_1 ASV_8 ASV_3 ASV_11 ASV_41 ASV_5 ASV_14
## 0.1559092 0.2493925 0.3120212 0.3469385 0.3763396 0.4001384 0.4230282 0.4418947
## ASV_13 ASV_4 ASV_7 ASV_6 ASV_143 ASV_37 ASV_295 ASV_74
## 0.4591820 0.4753803 0.4906218 0.5033763 0.5156251 0.5253461 0.5347415 0.5433613
## ASV_595 ASV_21 ASV_108 ASV_93 ASV_12 ASV_280 ASV_48 ASV_25
## 0.5515659 0.5596323 0.5676049 0.5745665 0.5810373 0.5867747 0.5921312 0.5974654
## ASV_103 ASV_46 ASV_80 ASV_105 ASV_19 ASV_191 ASV_395 ASV_56
## 0.6021234 0.6062252 0.6101371 0.6140439 0.6177333 0.6213059 0.6248227 0.6282580
## ASV_571 ASV_51 ASV_43 ASV_596 ASV_912 ASV_622 ASV_378 ASV_457
## 0.6315415 0.6348044 0.6379717 0.6410716 0.6441469 0.6470837 0.6500205 0.6529518
## ASV_277 ASV_542 ASV_202 ASV_160 ASV_239 ASV_29 ASV_161 ASV_676
## 0.6558080 0.6586233 0.6613988 0.6641647 0.6668042 0.6694124 0.6719872 0.6745569
## ASV_288 ASV_442 ASV_702 ASV_367 ASV_86 ASV_1087 ASV_286 ASV_721
## 0.6770678 0.6795151 0.6819421 0.6843573 0.6867722 0.6891790 0.6915594 0.6938843
## ASV_590 ASV_733 ASV_547
## 0.6961563 0.6984201 0.7006448
##
## $`0_5`
## ASV_1 ASV_2 ASV_3 ASV_15 ASV_41 ASV_35 ASV_11 ASV_43
## 0.1596402 0.2769144 0.3660115 0.4096160 0.4458896 0.4776920 0.5074776 0.5333649
## ASV_14 ASV_290 ASV_13 ASV_4 ASV_7 ASV_6 ASV_37 ASV_5
## 0.5525083 0.5715078 0.5889538 0.6046459 0.6195116 0.6324838 0.6426873 0.6505407
## ASV_21 ASV_93 ASV_884 ASV_47 ASV_206 ASV_12 ASV_192 ASV_46
## 0.6582921 0.6653665 0.6721461 0.6776372 0.6828789 0.6873721 0.6916158 0.6957841
## ASV_268 ASV_302
## 0.6997072 0.7035527
##
## $`0_7`
## ASV_1 ASV_2 ASV_3 ASV_11 ASV_14 ASV_13 ASV_8 ASV_4
## 0.3638775 0.5050852 0.5453576 0.5786506 0.6000419 0.6195454 0.6370942 0.6546343
## ASV_7 ASV_41 ASV_6
## 0.6712497 0.6860534 0.7005586
##
## $`0_21`
## ASV_1 ASV_2 ASV_3 ASV_15 ASV_41 ASV_11 ASV_14 ASV_13
## 0.2439092 0.3713429 0.4107600 0.4455105 0.4801039 0.5123250 0.5330289 0.5519011
## ASV_4 ASV_5 ASV_7 ASV_37 ASV_6 ASV_21 ASV_563 ASV_93
## 0.5688735 0.5849634 0.6010376 0.6169260 0.6309642 0.6393475 0.6476806 0.6553317
## ASV_77 ASV_75 ASV_25 ASV_84 ASV_90 ASV_101 ASV_774
## 0.6629557 0.6705305 0.6775874 0.6842098 0.6902303 0.6961905 0.7015975
##
## $`0_35`
## ASV_1 ASV_2 ASV_3 ASV_11 ASV_25 ASV_14 ASV_13 ASV_4
## 0.3160318 0.4524028 0.4918565 0.5249752 0.5558200 0.5771055 0.5965077 0.6139569
## ASV_15 ASV_7 ASV_41 ASV_6 ASV_43 ASV_37 ASV_5
## 0.6307615 0.6472906 0.6617923 0.6762249 0.6883021 0.6992860 0.7083899
##
## $`1_3`
## ASV_2 ASV_8 ASV_1 ASV_7 ASV_11 ASV_41 ASV_5 ASV_37
## 0.1953861 0.3028605 0.3882193 0.4165535 0.4426971 0.4654072 0.4878189 0.5092063
## ASV_9 ASV_4 ASV_143 ASV_295 ASV_107 ASV_74 ASV_12 ASV_595
## 0.5284794 0.5475480 0.5611506 0.5729895 0.5825308 0.5920093 0.6011954 0.6103068
## ASV_108 ASV_29 ASV_13 ASV_28 ASV_6 ASV_280 ASV_48 ASV_22
## 0.6189996 0.6276851 0.6362907 0.6439800 0.6504982 0.6567543 0.6627028 0.6684749
## ASV_112 ASV_25 ASV_44 ASV_21 ASV_19 ASV_14
## 0.6741686 0.6798234 0.6853675 0.6908227 0.6961823 0.7015123
##
## $`1_5`
## ASV_2 ASV_1 ASV_3 ASV_8 ASV_15 ASV_35 ASV_41 ASV_43
## 0.1758637 0.3232713 0.3914464 0.4565280 0.5022665 0.5351720 0.5644499 0.5918955
## ASV_7 ASV_11 ASV_37 ASV_290 ASV_9
## 0.6176456 0.6426026 0.6632736 0.6830943 0.7014978
##
## $`1_7`
## ASV_1 ASV_2 ASV_8 ASV_7
## 0.3923688 0.5839276 0.6703706 0.7009005
##
## $`1_21`
## ASV_1 ASV_2 ASV_8 ASV_15 ASV_41 ASV_7 ASV_11 ASV_37
## 0.2452798 0.4185032 0.4950443 0.5334728 0.5692247 0.5985179 0.6269086 0.6540209
## ASV_9 ASV_4 ASV_5
## 0.6761574 0.6957824 0.7074032
##
## $`1_35`
## ASV_1 ASV_2 ASV_8 ASV_25 ASV_7 ASV_11 ASV_37
## 0.3289997 0.5113005 0.5884027 0.6221849 0.6526897 0.6822548 0.7064413
##
## $`3_5`
## ASV_1 ASV_2 ASV_3 ASV_8 ASV_15 ASV_41 ASV_35 ASV_43
## 0.1354159 0.2632723 0.3262863 0.3875957 0.4295800 0.4694661 0.4998048 0.5245169
## ASV_5 ASV_290 ASV_143 ASV_295 ASV_74 ASV_595 ASV_108 ASV_884
## 0.5433889 0.5616783 0.5736603 0.5828478 0.5911394 0.5991652 0.6068150 0.6133412
## ASV_12 ASV_280 ASV_47 ASV_48 ASV_25 ASV_206 ASV_103 ASV_192
## 0.6191171 0.6246384 0.6299071 0.6351469 0.6402671 0.6452997 0.6497959 0.6541620
## ASV_80 ASV_105 ASV_268 ASV_302 ASV_123 ASV_191 ASV_162 ASV_571
## 0.6579990 0.6617961 0.6655726 0.6692926 0.6728606 0.6763398 0.6796543 0.6828663
## ASV_333 ASV_19 ASV_596 ASV_324 ASV_202 ASV_622
## 0.6860621 0.6892236 0.6922560 0.6952681 0.6981681 0.7010409
##
## $`3_7`
## ASV_1 ASV_2 ASV_8 ASV_41 ASV_5 ASV_143 ASV_15 ASV_295
## 0.3847470 0.5278730 0.5984213 0.6190516 0.6395609 0.6519637 0.6635236 0.6730590
## ASV_74 ASV_595 ASV_108 ASV_20
## 0.6816860 0.6900158 0.6979523 0.7052822
##
## $`3_21`
## ASV_1 ASV_2 ASV_8 ASV_41 ASV_15 ASV_5 ASV_143 ASV_295
## 0.2551226 0.3825979 0.4491097 0.4841839 0.5175521 0.5403000 0.5532157 0.5631301
## ASV_74 ASV_25 ASV_595 ASV_75 ASV_77 ASV_108 ASV_563 ASV_84
## 0.5721107 0.5807859 0.5894468 0.5980167 0.6065245 0.6147941 0.6227978 0.6302389
## ASV_37 ASV_90 ASV_101 ASV_105 ASV_12 ASV_280 ASV_117 ASV_48
## 0.6370426 0.6438388 0.6504915 0.6569526 0.6629932 0.6689257 0.6747475 0.6803654
## ASV_119 ASV_774 ASV_127 ASV_103
## 0.6859122 0.6911055 0.6962877 0.7012021
##
## $`3_35`
## ASV_1 ASV_2 ASV_8 ASV_25 ASV_41 ASV_5 ASV_15 ASV_143
## 0.3379849 0.4693596 0.5341328 0.5594090 0.5804469 0.5997972 0.6152378 0.6278968
## ASV_43 ASV_295 ASV_74 ASV_595 ASV_108 ASV_20 ASV_280 ASV_12
## 0.6380531 0.6477597 0.6565787 0.6650580 0.6731471 0.6803829 0.6861910 0.6917535
## ASV_48 ASV_64
## 0.6972893 0.7023603
##
## $`5_7`
## ASV_1 ASV_2 ASV_3 ASV_15 ASV_35 ASV_41 ASV_43
## 0.3401562 0.4679233 0.5512435 0.6037216 0.6440680 0.6812394 0.7147328
##
## $`5_21`
## ASV_1 ASV_2 ASV_3 ASV_41 ASV_15 ASV_35 ASV_43 ASV_290
## 0.2356434 0.3355258 0.4160595 0.4747834 0.5300460 0.5688651 0.6010316 0.6244334
## ASV_5 ASV_563 ASV_77 ASV_75 ASV_884 ASV_25 ASV_37 ASV_84
## 0.6369174 0.6464076 0.6550903 0.6637170 0.6720674 0.6801164 0.6880977 0.6956398
## ASV_90
## 0.7024963
##
## $`5_35`
## ASV_1 ASV_2 ASV_3 ASV_15 ASV_35 ASV_43 ASV_41 ASV_25
## 0.3057972 0.4266802 0.5112698 0.5643554 0.6051066 0.6429414 0.6795083 0.7152297
##
## $`7_21`
## ASV_1 ASV_2 ASV_41 ASV_15 ASV_8 ASV_5 ASV_563 ASV_77
## 0.3399139 0.5154741 0.5737377 0.6270493 0.6616425 0.6804544 0.6952852 0.7088542
##
## $`7_35`
## ASV_1 ASV_2 ASV_25 ASV_8
## 0.3488067 0.6023353 0.6758181 0.7163741
##
## $`21_35`
## ASV_1 ASV_2 ASV_41 ASV_15 ASV_25 ASV_5 ASV_43 ASV_563
## 0.3096708 0.4555386 0.5107610 0.5639702 0.6116831 0.6305893 0.6487705 0.6629220
## ASV_77 ASV_75 ASV_37
## 0.6758696 0.6887334 0.7007630##tank 3c # Beta Diversity and Hierachical clustering tank 3c & similarity percentages (SIMPER)
##
## Call:
## adonis(formula = final_ps_bray ~ Sampling_day + Fish_ID, data = sampledf)
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## Sampling_day 6 2.9511 0.49186 1.6938 0.21770 0.001 ***
## Fish_ID 1 0.4413 0.44132 1.5198 0.03256 0.022 *
## Residuals 35 10.1635 0.29039 0.74974
## Total 42 13.5560 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] 0 0 0 0 0 0 0 0 1 1 1 1 1 3 3 3 3 3 3 5 5 5 5 5 5
## [26] 7 7 7 7 7 7 21 21 21 21 21 21 21 35 35 35 35 35
## Levels: 0 1 3 5 7 21 35
## [1] 43 1021## [1] 43 17## [1] 43 17## cumulative contributions of most influential species:
##
## $`0_1`
## ASV_1 ASV_3 ASV_2 ASV_7 ASV_4 ASV_10 ASV_27 ASV_36
## 0.1843219 0.3063645 0.4185268 0.4828998 0.5386187 0.5919498 0.6410502 0.6696057
## ASV_5 ASV_6
## 0.6959016 0.7171252
##
## $`0_3`
## ASV_1 ASV_2 ASV_7 ASV_4 ASV_41 ASV_10 ASV_15 ASV_9
## 0.2347052 0.3084465 0.3736001 0.4299581 0.4792767 0.5271546 0.5718236 0.6066422
## ASV_5 ASV_290 ASV_6 ASV_21 ASV_3
## 0.6347586 0.6554449 0.6758527 0.6956885 0.7140231
##
## $`0_5`
## ASV_1 ASV_15 ASV_2 ASV_41 ASV_7 ASV_4 ASV_10 ASV_5
## 0.1843774 0.3227982 0.4430433 0.5002742 0.5479178 0.5890501 0.6227381 0.6416406
## ASV_6 ASV_21 ASV_3 ASV_613 ASV_14
## 0.6565899 0.6710815 0.6855019 0.6994655 0.7116222
##
## $`0_7`
## ASV_1 ASV_2 ASV_7 ASV_4 ASV_10 ASV_69 ASV_5 ASV_58
## 0.3462517 0.4364703 0.4978136 0.5508450 0.5942198 0.6366886 0.6598294 0.6819491
## ASV_172
## 0.7017261
##
## $`0_21`
## ASV_1 ASV_2 ASV_7 ASV_4 ASV_10 ASV_5 ASV_31
## 0.4165823 0.4974243 0.5637314 0.6210540 0.6679291 0.6927811 0.7163749
##
## $`0_35`
## ASV_1 ASV_2 ASV_7 ASV_3 ASV_4 ASV_10 ASV_9 ASV_5
## 0.2194957 0.3390156 0.4040006 0.4611365 0.5173163 0.5632718 0.5979512 0.6226659
## ASV_17 ASV_6 ASV_21 ASV_14
## 0.6438854 0.6643603 0.6841266 0.7012104
##
## $`1_3`
## ASV_1 ASV_3 ASV_2 ASV_27 ASV_41 ASV_15 ASV_9 ASV_10
## 0.1960699 0.3196556 0.4403038 0.4926174 0.5399117 0.5863423 0.6222812 0.6549650
## ASV_36 ASV_290
## 0.6855713 0.7077207
##
## $`1_5`
## ASV_1 ASV_2 ASV_15 ASV_3 ASV_41 ASV_27 ASV_10 ASV_36
## 0.1854246 0.3275673 0.4681287 0.5539115 0.6139536 0.6501457 0.6720877 0.6932479
## ASV_613
## 0.7074061
##
## $`1_7`
## ASV_1 ASV_2 ASV_3 ASV_27 ASV_69 ASV_10
## 0.3442872 0.4715041 0.5836696 0.6312931 0.6752980 0.7047229
##
## $`1_21`
## ASV_1 ASV_2 ASV_3 ASV_27
## 0.4083423 0.5378712 0.6577839 0.7087125
##
## $`1_35`
## ASV_1 ASV_3 ASV_2 ASV_27 ASV_9 ASV_10 ASV_36 ASV_17
## 0.1825084 0.3383051 0.4867232 0.5416513 0.5796768 0.6136729 0.6457874 0.6697269
## ASV_14 ASV_68
## 0.6869210 0.7037464
##
## $`3_5`
## ASV_1 ASV_15 ASV_2 ASV_41 ASV_9 ASV_290 ASV_613 ASV_113
## 0.2550408 0.3996110 0.5239419 0.6045151 0.6284162 0.6455828 0.6614439 0.6752702
## ASV_495 ASV_848 ASV_5
## 0.6871647 0.6964440 0.7047446
##
## $`3_7`
## ASV_1 ASV_2 ASV_69 ASV_41 ASV_15 ASV_9 ASV_58 ASV_172
## 0.3354193 0.4411649 0.4975079 0.5519658 0.6015560 0.6375958 0.6669382 0.6931776
## ASV_290
## 0.7189947
##
## $`3_21`
## ASV_1 ASV_2 ASV_15 ASV_41 ASV_9 ASV_31 ASV_290
## 0.3739827 0.4673603 0.5339512 0.5976185 0.6432654 0.6779688 0.7081700
##
## $`3_35`
## ASV_1 ASV_2 ASV_3 ASV_9 ASV_15 ASV_41 ASV_17 ASV_290
## 0.2344869 0.3822032 0.4387048 0.4940174 0.5464978 0.5975971 0.6223389 0.6463747
## ASV_113 ASV_305 ASV_68
## 0.6657336 0.6832495 0.7007528
##
## $`5_7`
## ASV_1 ASV_15 ASV_2 ASV_41 ASV_69 ASV_58
## 0.3283242 0.4717843 0.5933095 0.6576198 0.6932746 0.7118302
##
## $`5_21`
## ASV_1 ASV_15 ASV_2 ASV_41
## 0.3897932 0.5475185 0.6543034 0.7205945
##
## $`5_35`
## ASV_1 ASV_2 ASV_15 ASV_41 ASV_3 ASV_9 ASV_17 ASV_613
## 0.2194831 0.3889882 0.5368303 0.5987786 0.6366637 0.6630294 0.6793146 0.6939320
## ASV_68
## 0.7074731
##
## $`7_21`
## ASV_1 ASV_2 ASV_69 ASV_31 ASV_58
## 0.3658662 0.5305994 0.6215347 0.6689625 0.7163281
##
## $`7_35`
## ASV_1 ASV_2 ASV_3 ASV_69 ASV_9 ASV_58 ASV_17
## 0.3633045 0.5217774 0.5760059 0.6265699 0.6654838 0.6918212 0.7156709
##
## $`21_35`
## ASV_1 ASV_2 ASV_3 ASV_9
## 0.4311703 0.6137946 0.6751535 0.7184669